Background: Infective endocarditis (IE) represents a major complication in patients with congenital heart disease (CHD) and is associated with high morbidity and mortality. The aim of this study was to analyse the frequency and outcome of IE in contemporary CHD patients based on all IE hospital admissions in Germany over a 10-year period. Methods: Based on data of all hospital admissions in Germany from 2009 to 2018, we identified all CHD cases with a diagnosis of IE. The data contained information on patient demographics, diagnoses, surgical procedures, and mortality. The primary endpoint of the study was endocarditis-associated mortality as well as major adverse events (defined as death or myocardial infarction, stroke, pulmonary embolism, sepsis, renal dialysis, resuscitation, or intubation). Results: Overall, 309,245 CHD inpatient cases were included in the analysis (underlying heart defects of simple complexity 55%, moderate complexity 23%, and complex heart defects 22%, respectively). Of those, 2512 (0.8% of all inpatient cases) were treated for IE. The mortality rate of IE inpatient cases was 6% with a major adverse events rate of 46%, and 41.5% of cases required surgical intervention. The overall IE associated mortality was lower in adult CHD cases compared to the 153,242 in adult IE cases without CHD (7.1% vs. 16.1%, p < 0.001). After adjustments using multivariable logistic regression analysis, the presence or complexity of CHD was not associated with the outcomes. Meanwhile, age, male sex, and co-morbidities emerged as significant predictors of adverse outcomes. Conclusions: IE accounts for a minority of CHD related hospitalizations but remains a deadly disease, and major adverse events are common in this setting. Due to different demographic and co-morbidity spectrums, adult CHD patients tend to have better survival prospects when compared to non-CHD IE patients. Acquired co-morbidities emerged as the main predictors of adverse outcomes.